Based on your input up to this point, this is what I would do.
1. if you are not a tinkerer or you have a highly-mixed environment (i.e. macs), buy a copy of WHS and put it on your atom build. Use it only as a Media Server/NAS. Go Linux if you are on a tight budget and are willing to live with core functionality -- you don't need anything fancy, or you enjoy building things using a command line.
2. build another machine with tuner/encoder. This machine should have a minimum 2.5GHz dual-core cpu. An atom isn't going to cut it. I don't even think Pinetrail is of much use to you. Use Windows since you say one of your priorities is maximum compatibility with tuners. Linux really cannot claim to be highly compatible with tuners. [Note that you should ignore everything I've said here if your priorities are encrypted-QAM (cable).]
If you plan to do heavy processing on this machine (rips and transcoding), go 4-core, but now you probably need to move this machine to the basement due to the noise.
Go green drives if the machine is going to be near you while you are watching TV. Go 7,200 drives if the machine is tucked away, or you plan on using raid. There would be little need to stick more than 1 or 2 terabytes into this build -- that is what the media server is for.
On the other hand, if you want to capture encrypted-QAM, go either Tivo or Miro. You will not be able to build a cheaper box.
This is the software I would look at.
For front-end duties, check out XBMC and Boxee. They both can be operated with a remote. Win 7 with Windows Media Center has both front-end and back-end capability, and supports a wide array of tuner hardware.
Also check out Sage TV.
You have probably noticed that we are in the midst of shifting away from traditional cable and towards internet-TV.
This is just conjecture, but I expect most people who want to build a box with a tuner eventually give up that pursuit once they understand the problems with encrypted-QAM. [I can go into detail if you would find that helpful.] If their needs are narrow, however, the idea has merit. For example, if you want to restrict your HTPC to OTA or unencrypted-QAM, then its viable -- better solutions exist otherwise.
If the discussion above didn't answer your questions, please answer the following. Your odds of getting a response that meets your needs go up.
1. do you want to incorporate blu-ray into this build? This has a major impact on the direction of your build so give it some thought.
2. are you a detail-oriented person who likes to tinker? do you mind compiling software? do you mind doing a bunch of googling and reading?
3. what is your budget?
4. what signals are you interested in capturing? OTA (over-the-air), clear-QAM (unencrypted cable), encrypted-QAM, analog, or something else?
5. have you thought about your front-end? Do you want your front-end and back-end in the same box? are you looking to use a 10' interface (aka a remote, or bluetooth/RF keyboard)? Or do you have your front-end already figured out?
6. do you own or plan to buy an a/v receiver?
7. do you own or plan to buy a home theater? If so, how many speakers do you plan on using?
8. do you have any special audio requirements? Are you an audiophile? Are you a big movie person who really wants to simulate the movie experience? or are you like most of us who don't fall into those categories and are not willing to spend the extra scratch?
9. where will the box with the tuner/encoder be located? will it be within your line-of-sight when you use your home theater, or will it be tucked away?
10. do you expect your environment that the media server has to interact with to change in the future? i.e., do you have plans to add macs?
11. does computer noise bother you while you are watching a movie, or would you prefer maximum speed? what are your priorities? there are trade-offs.
12. what is your time frame? are you putting something together in the next few days, or can you wait?
13. how much does flash figure in? Do you plan on watching hulu and youtube with this setup?
NOTE that CES is meeting and that it's likely that something interesting that affects your decision will be announced in the next few days. For example, this was recently announced and I think it's going to have a large impact once people understand its significance:
http://www.engadget.com/2010/01/05/hands-on-with-the-boxee-box/
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